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ANNOgesic is the swiss army knife for RNA-Seq based annotation of bacterial/archaeal genomes.
It is a modular, command-line tool that can integrate different types of RNA-Seq data based on dRNA-Seq
(differential RNA-Seq) or RNA-Seq protocols that inclusde transcript fragmentation to generate high quality
genome annotations. It can detect more than 20 genomic features. The tool was heavily tested with several RNA-Seq
data set from bacterial as well as archaeal samples.
SPROTify is a machine learning–based tool for accurate small-protein prediction using features derived from amino acid sequences and secondary structure information.
SPROTify is trained on a curated dataset of experimentally validated small proteins, with multiple algorithms assessed through 5-fold cross-validation and further
optimized via hyperparameter tuning. The tool integrates five classification models—LGBMClassifier, BaggingClassifier, XGBClassifier, ExtraTreesClassifier,
and SVC—allowing users to select the most suitable model based on their analytical goals. SPROTify demonstrates high performance, achieving 92% accuracy,
92% F1-score, and 96% AUC on an independent test set.
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Collaboration